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Yorodumi- EMDB-13057: Structure of the AI-2 exporter family protein YdiK from E. coli -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13057 | |||||||||
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Title | Structure of the AI-2 exporter family protein YdiK from E. coli | |||||||||
Map data | Final single particle EM map | |||||||||
Sample |
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Keywords | cryo-EM / membrane protein / autoinducer-2 exporter / quorum sensing / pentamer / protein oligomerization / STRUCTURAL PROTEIN / AI-2E / transporter | |||||||||
Function / homology | Transmembrane protein TqsA-like / AI-2E family transporter / plasma membrane / Putative transport protein YdiK Function and homology information | |||||||||
Biological species | Escherichia coli (strain K12) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Khera R / Xie H | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: EMBO J / Year: 2022 Title: Cryo-EM structures of pentameric autoinducer-2 exporter from Escherichia coli reveal its transport mechanism. Authors: Radhika Khera / Ahmad R Mehdipour / Jani R Bolla / Joerg Kahnt / Sonja Welsch / Ulrich Ermler / Cornelia Muenke / Carol V Robinson / Gerhard Hummer / Hao Xie / Hartmut Michel / Abstract: Bacteria utilize small extracellular molecules to communicate in order to collectively coordinate their behaviors in response to the population density. Autoinducer-2 (AI-2), a universal molecule for ...Bacteria utilize small extracellular molecules to communicate in order to collectively coordinate their behaviors in response to the population density. Autoinducer-2 (AI-2), a universal molecule for both intra- and inter-species communication, is involved in the regulation of biofilm formation, virulence, motility, chemotaxis, and antibiotic resistance. While many studies have been devoted to understanding the biosynthesis and sensing of AI-2, very little information is available on its export. The protein TqsA from Escherichia coli, which belongs to the AI-2 exporter superfamily, has been shown to export AI-2. Here, we report the cryogenic electron microscopic structures of two AI-2 exporters (TqsA and YdiK) from E. coli at 3.35 Å and 2.80 Å resolutions, respectively. Our structures suggest that the AI-2 exporter exists as a homo-pentameric complex. In silico molecular docking and native mass spectrometry experiments were employed to demonstrate the interaction between AI-2 and TqsA, and the results highlight the functional importance of two helical hairpins in substrate binding. We propose that each monomer works as an independent functional unit utilizing an elevator-type transport mechanism. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13057.map.gz | 40 MB | EMDB map data format | |
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Header (meta data) | emd-13057-v30.xml emd-13057.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13057_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_13057.png | 111.9 KB | ||
Masks | emd_13057_msk_1.map | 52.7 MB | Mask map | |
Filedesc metadata | emd-13057.cif.gz | 5.7 KB | ||
Others | emd_13057_half_map_1.map.gz emd_13057_half_map_2.map.gz | 40.4 MB 40.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13057 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13057 | HTTPS FTP |
-Validation report
Summary document | emd_13057_validation.pdf.gz | 702.3 KB | Display | EMDB validaton report |
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Full document | emd_13057_full_validation.pdf.gz | 701.9 KB | Display | |
Data in XML | emd_13057_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | emd_13057_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13057 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13057 | HTTPS FTP |
-Related structure data
Related structure data | 7ot9MC 7nb6C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13057.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Final single particle EM map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.108 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_13057_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map1
File | emd_13057_half_map_1.map | ||||||||||||
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Annotation | Half map1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map2
File | emd_13057_half_map_2.map | ||||||||||||
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Annotation | Half map2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Pentameric YdiK
Entire | Name: Pentameric YdiK |
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Components |
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-Supramolecule #1: Pentameric YdiK
Supramolecule | Name: Pentameric YdiK / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
Molecular weight | Theoretical: 199 KDa |
-Macromolecule #1: AI-2E member YdiK
Macromolecule | Name: AI-2E member YdiK / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
Molecular weight | Theoretical: 39.865891 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MVNVRQPRDV AQILLSVLFL AIMIVACLWI VQPFILGFAW AGTVVIATWP VLLRLQKIMF GRRSLAVLVM TLLLVMVFII PIALLVNSI VDGSGPLIKA ISSGDMTLPD LAWLNTIPVI GAKLYAGWHN LLDMGGTAIM AKVRPYIGTT TTWFVGQAAH I GRFMVHCA ...String: MVNVRQPRDV AQILLSVLFL AIMIVACLWI VQPFILGFAW AGTVVIATWP VLLRLQKIMF GRRSLAVLVM TLLLVMVFII PIALLVNSI VDGSGPLIKA ISSGDMTLPD LAWLNTIPVI GAKLYAGWHN LLDMGGTAIM AKVRPYIGTT TTWFVGQAAH I GRFMVHCA LMLLFSALLY WRGEQVAQGI RHFATRLAGV RGDAAVLLAA QAIRAVALGV VVTALVQAVL GGIGLAVSGV PY ATLLTVL MILSCLVQLG PLPVLIPAII WLYWTGDTTW GTVLLVWSGV VGTLDNVIRP MLIRMGADLP LILILSGVIG GLI AFGMIG LFIGPVLLAV SWRLFAAWVE EVPPPTDQPE EILEELGEIE KPNK UniProtKB: Putative transport protein YdiK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.8 mg/mL |
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Buffer | pH: 7.5 / Details: 50 mM Tris (pH 7.5), 150 mM NaCl and 0.006% GDN |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III / Details: blot time 4 s, blot force +20. |
Details | Its a membrane protein and for purification, glyco-diosgenin was used. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 7378 / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |